Treading in black waters means you are fighting or argueing with someone and you are JUST on the verge of telling them to fuck off. You can only use this term when you are about to end an arguement or a friendship/agreement. Should be used if you are completley ready to lose this persons trust and affection.

After James starting being a smartass and splitting hairs with me about how the server operated, I warned him he was treading in black waters.